Second harmonic generation (SHG) polarization microscopy was used to investigate the organization of myosin nanomotors in myofilaments of muscle cells. The distribution of the second-order nonlinear susceptibility component ratio χzzz(2)/χzxx(2) along anisotropic bands of sarcomeres revealed differences between the headless and head-containing regions of myofilaments. The polarization-in polarization-out SHG measurements of headless myosin mutants of indirect flight muscle in Drosophila melanogaster confirmed a lower susceptibility component ratio compared to the head-containing myocytes with wild-type myosins. The increase in the ratio is assigned to the change in the deflection angle of the myosin S2 domain and possible contribution of myosin heads. The nonlinear susceptibility component ratio is a sensitive indicator of the myosin structure, and therefore, it can be used for conformational studies of myosin nanomotors. The measured ratio values can also be used as the reference for ab initio calculations of nonlinear optical properties of different parts of myosins.